R: The v5 'Assay' Object

Assay5-class {SeuratObject}

R Documentation

The v5 `Assay` Object

The v5 Assay is the typical Assay class used in Seurat v5; ...

layers: A named list containing expression matrices; each matrix should be a two-dimensional object containing some subset of cells and features defined in the cells and features slots. Cell and feature membership is recorded in the cells and features slots, respectively
cells: A logical mapping of cell names and layer membership; this map contains all the possible cells that this assay can contain. New layers must have some subset of cells present in this map
features: A logical mapping of feature names and layer membership; this map contains all the possible features that this assay can contain. New layers must have some subset of features present in this map
default: A one-length integer with the end index of the default layer; the default layer be all layers up to and including the layer at index default
assay.orig: Original assay that this assay is based off of; used to track assay provenance
meta.data: A data frame with feature-level meta data; should have the same number of rows as features
misc: A named list of unstructured miscellaneous data
key: A one-length character vector with the object's key; keys must be one or more alphanumeric characters followed by an underscore “_” (regex pattern “^[a-zA-Z][a-zA-Z0-9]*_$”)